So I just got my Fender Deluxe Strat Plus for my birthday and I decided to slap some 11's on there because thats what I normally use on all my guitars. It's got a two point tremolo so it can go up and down.

Now when I put these on and tuned em up, the bridge came up a lot higher than it did on 9's

Is this a problem? Can I damage the guitar playing like this or do I need to go back to 9's or 10's

You have to have it set up when you change string sizes. Just go back to 9's until you can have it set up for 11's.
No, you don't have to get it set up.

What you do is put the 11's on, and screw in the two "claw" (i think they are called) screws in the trem cavity in the back untill the trem is leveled, then re-tune.

It is very simple, I went from 9's to 11's on my strat as well.

You might want to file out your nut a bit too so the low E and A can fit.
I have to adjust the bridge tension screws everytime I change string brands, even if its the same guage. Its normal.

I learned this from a professional:
Tighten your bridge until it lays flat on the body, and so that if you press down on the bridge, the tone will not be raised. Then, make adjustments on the screws so that the bridge will remain steady on the body until you reach a whole-step bend on the G string, at which time the bridge should start to raise a bit.

Contrary to Suicidal_brick, you DO need to get your guitar "set-up" every once and awhile if you use thick strings. The increased tension on the neck will bend the fretboard MUCH quicker over the months than if you were using 10's, let alone 9's.
Going from 9's to 11's is a HUGE jump

Unless you want to warp the neck slowly go get it set up for 11ga

Or take the risk and simply tighten the trem screws until the floater is even and straight